Workshop on Methods and Applications of Molecular Dynamics to Biopolymers

Instructors: Dr. Charles L. Brooks III , The Scripps Research Institute
  Dr. Michael Crowley, The Scripps Research Institute
  Dr. Alexander D. MacKerell, Jr., University of Maryland at Baltimore
  Nilesh Banavali, University of Maryland at Baltimore

A complete agenda follows the list of lectures and tutorials.

 

Lectures Tutorials
Overview of Molecular Modeling and Dynamics (PDF file, 2.8 Mb)   Building and Conditioning Macromolecular Structures for Proteins
Periodic Boundaries, Non-bond Interactions and PME (PDF file, 4.6 Mb)    
Simulations of Nucleic Acids and Lipids (PDF file, 61K)   Building and Conditioning Macromolecular Structures for DNA
    Building and Conditioning Macromolecular Structures for Membranes
Conformational Search, Structure, and Trajectory Analysis (PDF file, 3.4 Mb)    
Strategies for Parameter Development (PDF file, 71K)   Parameterization of Molecules
Free Energy Simulations (PDF file, 3.4 Mb)   Free Energy Calculations
Hybrid Quantum Mechanical/Molecular Mechanical Methods (PDF file, 27K)   Hybrid Quantum Mechanical/Molecular Mechanical Calcuations
Merck Molecular Force Field (PDF file, 23K)   Merck Molecular Force Field Calculations

 

Final Agenda
 June 4 -7, 2000


Sunday June 4th

1:00 - 1:15   Welcome, administrative details Troy Wymore
1:15 - 1:45   Introduction & overview of biomedical computing at PSC David Deerfield
1:45 - 2:00   Break  
2:00 - 3:00   Introduction to the PSC environment: UNIX, AFS, file archiving, Cray T3E Tom Maiden
3:00 - 5:00   Computer Laboratory:
Tutorials, setting up a working environment for the workshop		  


Monday June 5th

8:30 - 9:00   Continental breakfast  
9:00 - 9:15   Welcoming remarks Ralph Roskies, Scientific Director
9:15 - 10:15   Overview of molecular modeling and dynamics
(PDF file, 2.8Mb)		 Charles Brooks
10:15 - 10:30   Break  
10:30 - 11:30   Periodic boundaries, nonbond interactions, and PME
(PDF file, 4.6 Mb)		 Michael Crowley
11:30 - 12:30   Simulations of nucleic acids and lipids
(PDF file, 61K)		 Alex MacKerell
12:30 - 2:00   Lunch and poster session  
2:00 - 4:00   Hands on session building and "conditioning" macromolecular structures
 
4:00 - 4:15   Break  
4:15 - 5:15   Conformational search, Structure and trajectory analysis
(PDF file, 3.4 Mb)		 Michael Crowley


Tuesday, June 6th


8:30 - 9:00   Continental breakfast  
9:00 - 10:30   Strategies for parameter development
(PDF file, 71K)		 Alex MacKerell
10:30 - 10:45   Break  
10:45 - 12:15   Computer laboratory  
12:15 - 1:30   Lunch  
1:30 - 2:45   Free energy simulations
(PDF file, 3.4 Mb)		 Charles Brooks
2:45 - 3:00   Break  
3:00 - 5:15   Computer laboratory: CHARMM Examples  
    Break for dinner  
7:00 - 9:00   Trip to the Westinghouse machine room facility  


Wednesday June 7th

8:30 - 9:00   Breakfast  
9:00 - 10:00   Quantum mechanical / molecular mechanical hybrid methods
(PDF file, 27K) and
Merck molecular force field
(PDF file, 23K) 		Alex MacKerell
10:15 - 11:45   Question/answer and discussion session or computer lab  
11:45 - Noon   Evaluations  
Noon - 1:00   Lunch  
Afternoon   Optional hands-on